Updated in Aug/22/2016

Here I will teach How to set the environment in Mac

1. (install the Xcode and Xcode-command-tool.)[http://railsapps.github.io/xcode-command-line-tools.html]

2. (install the MacPort)[https://www.macports.org/install.php]
   update MacPort by this command

   1	sudo port -v selfupdate

3. Tried to install PyMOL by MacPort

   1	sudo port install pymol

   And following the tips in the warning to install the python

   1	find ~/ -type f -name "_cmd.so"

   eg: return

   1	/opt//local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymol/_cmd.so

   Try to add the path of folder of pymol in the PYTHONPATH
   eg: /opt//local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/

   1 2	PYTHONPATH="/opt//local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages" export PYTHONPATH

Abstract:

This Series of blog pages is about the Script of PyMOL. If you are an expert of PyMOL/Python and give me some suggestions or find some errors in this page, I will be very happpppy. This is my First time to use PyMOL

Since the Dr.Marcelo Marcet-Palacios only provide a exist file of PyMOL software without a PyMOL API for Python. I am starting to setup the environment of Open-Source PyMOL, which take a long time(take care).

Setup Environment.

Dr.Marcelo Marcet-Palacios helped me to install the PyMOL by a Mac-package. However, I found the python script cannot load the PyMOL module. I started to find the reason.

https://www.biostars.org/p/113328/ helps a lot. If you want to

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import pymol

in your script, you wish you can install the pymol following the steps of installing an Open-Source PyMOL.

So I started to follow the http://www.pymolwiki.org/index.php/MAC_Install to install an Open-Source PyMOL. If your mac is over 10.5, my feedback is not use the fink, which is not easy to install.

Try this

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sudo port install tcl -corefoundation
sudo port install tk -quartz

sudo port install pymol

The other issue make me so annoying is that

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Traceback (most recent call last):
  File "/usr/local/Cellar/pymol/1.8.2.1/libexec/lib/python2.7/site-packages/pymol/__init__.py", line 72, in <module>
    import pymol
  File "/usr/local/Cellar/pymol/1.8.2.1/libexec/lib/python2.7/site-packages/pymol/__init__.py", line 536, in <module>
    import pymol._cmd
ImportError: dlopen(/usr/local/Cellar/pymol/1.8.2.1/libexec/lib/python2.7/site-packages/pymol/_cmd.so, 2): Library not loaded: /usr/local/opt/glew/lib/libGLEW.2.0.0.dylib
  Referenced from: /usr/local/Cellar/pymol/1.8.2.1/libexec/lib/python2.7/site-packages/pymol/_cmd.so
  Reason: image not found

I in my

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/usr/local/opt/glew/lib

It only has these following files:

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libGLEW.1.13.0.dylib	libGLEW.dylib		libGLEWmx.a
libGLEW.1.13.dylib	libGLEWmx.1.13.0.dylib	libGLEWmx.dylib
libGLEW.a		libGLEWmx.1.13.dylib	pkgconfig

The brew cannot upgrade the openGL. I have to update the XOs to the newest version. So I am downloading the package for 6 GB.

See you tomorrow. Hopefully, I could setup the environment.

Reference

https://www.biostars.org/p/113328/
http://www.pymolwiki.org/index.php/MAC_Install

Introduction

I have taken a Machine Learning Course at the University of Alberta. Our professor is Russell Greiner. We need to make a project and do some researches by Machine Learning method with our coach Koosha Golmohammadi. Since this is my first Machine Learning project. Soooo, this is not as good as some projects made by Machine Learning experts. However, we achieve a result is 90% accuracy which is closed to some the U.S agency in Boston.

1 Scraping Data.

We scraped some real estate data from real estate data website from Edmonton and marked in Edmonton Map.

2 Matching Data

Then we tried to match the real estate data with over 110 features in Open City Edmonton Data

It is a tough work there are different names for an address which is easier for the human to understand than a machine. After a little of the algorithm in nature language process(very basic).

we got the following useful data.

This is our first step for collating data and scraping data.

I will keep updating for Machine learning.
See you next time.

Our code resource

Ionic Development experience

When I was in 3rd year in Undergraduate, I has an opportunity to develop a Mobile Application. Since I have the experience of developing Android Mobile Application which is a CMPUT 301 course project. I build a team which from 2 different teams in 301 course.

The First Plan for us is build an Android Application by Java and an iOS Application by Object-C. The Customer asked us to finish in a half year. We don’t think that is enough to develop two Applications and test two.

We were looking for some solutions. The first solutions is Cordova Phonegap. However we searched some Phonegap products. The User experience and User Interface is much worse than an Application developed by Java or Object-C.

Then one of my team member ask his sister’s boyfriend who works in Google. He recommand the Ionic + Parse for our mobile application. That is the first time I heard about the Ionic.

Then I use Ionic + Parse to develop 3 Mobile Applications inculde one course project. It is not easy until we fully understand what the structure in the Ionic. Trust me! Ionic is a very clear Structure.

The Structure

In my Understanding the Ionic Stucture is like this form.

See you in next time.

integer factorization algorithm

1 Introduction

• note0 : Trivial Division use the trivial prime, which cannot use Miller-Rabin primality test
• note1 : Euler’s factorization method stops the algorithm

  when a number cannot found number = a^2 + b^2 = c^2 + d^2. 
  Miller-Rabin is only judge the prime not find the factors.
  

• note2 : Since I have not find a better way to find a number = a^2 + b^2 = c^2 + d^2.

  So Euler's spend on the this function I will list after that 
  

• note3 : In Pollards_rho Miller-Rabin primality test, inorder to handle some base cases. I use the

  trial_division to handle some special cases.
  

#Integer factorization:

1.1

Trial division: (Baseline)
This is a base line in my integer factorization algorithm project. It is using
a prime sieve for prime number generation which can judge a number is a prime or
continue do factorization.

Running time: in the worst case it is O(2^(n/2)/((n/2)*ln2))

• n is base-2 n digit number.

1.2

Euler’s factorization method:
This is an implementation factorization algorithm, which solves the following problem. Given an number, then find all prime factors. The base knowledge of Euler’s factorization is if
a number = a^2 + b^2 = c^2 + d^2. There is a quickly way to seperate into 2 factors.

Running time: It is very slow, worst case is greater than trial division,
only quick in some special cases and has potient quick.

1.3

Fermat’s factorization method:
This is an implementation factorization algorithm, which solves the following problem. Given an number, then find all prime factors. The base knowledge of Fermat’s factorization method:
is if a number = a^2 - b^2 There is a quickly way to seperate into 2 factors.

Running time: Worst case is O(N^{1/2})
General case is O(N^{1/3}) time.

1.4

Pollard’s rho algorithm:
This is an implementation factorization algorithm, which solves the following problem. Given an number, then find all prime factors. The base knowledge of Pollard’s rho algorithm is if a find
the abs(x^2+1-x) mod N if not 1 then it is a factor of N.

Running time: General case by the Birthday paradox in O(\sqrt p)\ <= O(n^{1/4})
but this is a heuristic claim, and rigorous analysis of the algorithm remains open.

2 A description of what sort of tests I have included

1 St: 2 primes production (each prime > million)

When the prime is very big, test the speed of each methods.

###1.1
The testcases: 15485867*32452867 = 502560782130689

###1.2
The testcases: 15487019*15487469 = 239854726664911

###1.3
The testcases: 15490781*67869427 = 1051350430252487

2 nd: 4 primes production (each prime between[1000,9999])

When the prime is big and more factors, test the speed of each methods.

###2.1
The testcases: 8147 8369 8623 * 7127 = 4190216175859403

###2.2
The testcases: 1259 1451 1613 * 1811 = 5336370322687

###2.3
The testcases: 6277 5351 8831 * 9733 = 2886979418455921

3 rd: over 6 small prime product

When the prime is not that big, but we have more factors for the number which need to be factorization.

###3.1
The testcases: 13 127 263 419 17 131 269 = 108990674873561

###3.2
The testcases: 13 17 2 1123 1426499 * 5 = 3540328013170

###3.3
The testcases: 547 701 29 149 5 * 2 = 16568744870

3 How to run the code:

There is a easy way to run by

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Then following the introduction. 

Firstly, you will see this introduction format.

integer factorization algorithm
type the number you want to run the algorithm
eg: 1
then will run the Trial division
1.Trial division
2.Euler’s factorization method
3.Fermat’s factorization method
4.Pollard’s rho algorithm
input the number:

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Then input the id of factorization method.

for the 3rd and 4th, you also need to choose the id of the prime generate method.

runner.py
-+—-1 “Trial division”—-+—“type number of testcases”
| +—“input the number which needs factorization”
|
|
+—-2 “Euler’s factorization method”—+—“type number of testcases”
| +—“input the number which needs factorization”
|
|
+—-3 “Fermat’s factorization method”—+—“type the prime generate method”
| +—1 “trivial prime”
| + +—“type number of testcases”
| | +—“input the number which needs factorization”
| |
| +—2 “Miller-Rabin primality test”
| +—“type number of testcases”
| +—“input the number which needs factorization”
|
|
+—-4 “Pollard’s rho algorithm”—+—“type the prime generate method”
+—1 “trivial prime”
| +—“type number of testcases”
| +—“input the number which needs factorization”
|
+—2 “Miller-Rabin primality test”
+—“type number of testcases”
+—“input the number which needs factorization”
```
Or

You can runner each single file
which has been listed:

Anything else you deem relevant.

1 I used the trivial prime:
which judge if a number is a prime.

2 I used another prime test called Miller-Rabin primality test:
which is much quicker and I have referenced in all my test cases. Prime test is correct.

Reference

http://www.bigprimes.net/archive/prime/10/

https://rosettacode.org/wiki/Miller–Rabin_primality_test#Python:_Probably_correct_answers

https://en.wikipedia.org/wiki/Integer_factorization

https://en.wikipedia.org/wiki/Trial_division

https://en.wikipedia.org/wiki/Fermat%27s_factorization_method

https://en.wikipedia.org/wiki/Pollard%27s_rho_algorithm

https://en.wikipedia.org/wiki/Euler%27s_factorization_method

http://mathworld.wolfram.com/PollardRhoFactorizationMethod.html

http://kadinumberprops.blogspot.ca/2012/11/fermats-factorization-running-time.html

HIV virus’s protine order like hexagon.
In the previous research, they working on the 2 dimension. However, in 3 dimension, the protine fills spherical surface.

This prgramming project is used to help the biology researcher to plot the HIV virus and get a list of all surface protine coordinations by setting the different radius.

The main structure.

If the point B rotated point A and get point C, I named points A is the father or root of B and C. As I mentioned that HIV virus’s surfaces protines order like a hexagen, protine will rotated 120 degree to get another protine.

There are a K_keepers list of points which generated and a Pivot list of points.

Use a Queue push in the points generated by the other 2 points, and push out the points which is already generated 2 points. When the distance is less than the protine’s radius, then the protines should not be placed at that coordination.

Reference:
https://en.wikipedia.org/wiki/Rotation_matrix

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